Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/7c56bea69291cab2762b0c66635b01/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/5504c8c331e3133b1f8b136cc39f67/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ab/5504c8c331e3133b1f8b136cc39f67/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/cc0594f4c6a73c399b831f18dc2930/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a0/7c56bea69291cab2762b0c66635b01/786-O_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz
==> STAGING COMPLETE (6 inputs)
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000
Done.
Execution Time = 0.12 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_pair_to_mini_genome_join.pl --fusions 786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusionreport.tsv --gtf /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_annot.gtf --genome_fa /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_genome.fa --out_prefix /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1 --shrink_introns --max_intron_length 1000
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/fusion_contigs.ok
Running: cp /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/cp_contigs_file_workdir
Running: cp /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/cp_gtf_file_workdir.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.bIDYTem8xp/cytoBand.txt
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fasta_and_gtf_to_cytoband.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.bIDYTem8xp/cytoBand.txt
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/cytoband.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed
-parsing GTF file: /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/gtf_gene_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/merged_contig_gtf_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.bedsort.ok
Running: bgzip -f /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.bgzip.ok
Running: tabix -p bed /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.sorted.bed.gz
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.bed.tabix.ok
Running: samtools faidx /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa
Execution Time = 0.00 minutes. CMD: samtools faidx /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/merged_contig_fai.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.bIDYTem8xp/fi_workdir --reads "/tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz"
* Running CMD: /usr/local/bin/STAR --runThreadN 8 --genomeDir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_genome.fa.star.idx --outSAMtype BAM SortedByCoordinate --twopassMode None --alignSJDBoverhangMin 10 --genomeSuffixLengthMax 10000 --limitBAMsortRAM 47271261705 --alignInsertionFlush Right --alignMatesGapMax 100000 --alignIntronMax 100000 --outSAMattributes All --readFilesIn /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz --genomeFastaFiles /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa --outSAMfilter KeepAllAddedReferences --sjdbGTFfile /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --alignSJstitchMismatchNmax 5 -1 5 5 --scoreGapNoncan -6 --readFilesCommand 'gunzip -c'
Jun 08 10:16:24 ..... started STAR run
Jun 08 10:16:24 ..... loading genome
Jun 08 10:18:08 ... generating Suffix Array index
Jun 08 10:22:02 ... completed Suffix Array index
Jun 08 10:22:02 ..... processing annotations GTF
Jun 08 10:22:03 ..... inserting junctions into the genome indices
Jun 08 10:23:05 ..... started mapping
Jun 08 11:25:03 ..... finished mapping
Jun 08 11:25:05 ..... started sorting BAM
Jun 08 11:25:06 ..... finished successfully
* Running CMD: mv Aligned.sortedByCoord.out.bam 786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
* Running CMD: samtools index 786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam
Execution Time = 68.76 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/run_FI_STAR.pl --genome /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir/ref_genome.fa --patch /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa --max_mate_dist 100000 -G /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --CPU 8 --out_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1.star --out_dir /tmp/nxf.bIDYTem8xp/fi_workdir --reads "/tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_2.fastp.fastq.gz"
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/run_STAR.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups
11:25:24 : INFO : Done.
Execution Time = 0.24 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/bam_mark_duplicates.py -i /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.sortedByCoord.out.bam -o /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --remove_dups
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/mark_dup_reads.ok
Running: samtools index /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/mark_dups_reads.index.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
-parsing GTF file: /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf
-parsing /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam
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[2530000] -done parsing /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam. Extracting junction info.
junction read elimination tally: $VAR1 = {
'seq-similar region overlap' => 9,
'low complexity anchor region' => 4,
'num_hits: 3 != num_counted_on_fusion_contigs 2 ' => 12,
'per_id < 96' => 14739,
'exons hit < 2' => 24,
'small anchor length' => 256,
'num_hits: 3 != num_counted_on_fusion_contigs 1 ' => 12,
'num_hits: 4 != num_counted_on_fusion_contigs 2 ' => 26,
'num_hits: 4 != num_counted_on_fusion_contigs 3 ' => 12,
' ** passed ** ' => 43594,
'num_hits: 2 != num_counted_on_fusion_contigs 1 ' => 529,
'num genes matched < 2' => 17,
'num_hits: 4 != num_counted_on_fusion_contigs 1 ' => 2,
'excessive soft clipping' => 16455
};
-writing fusion junction support info.
Execution Time = 1.72 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_JUNCTION_reads_from_fusion_contig_bam.pl --gtf_file /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/get_fusion_JUNCTION_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
-outputting the spanning read info: /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info.
- counting read alignments among fusion contigs.
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[159000] -fusion SPANNING read extraction for scaff: AC008969.1--SMARCA4
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[34000] -fusion SPANNING read extraction for scaff: ATAD2B--KLHL29
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[49000] -fusion SPANNING read extraction for scaff: BNC2--AL358117.1
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[34000] -fusion SPANNING read extraction for scaff: CENPU--ENPP6
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[69000] -fusion SPANNING read extraction for scaff: DHX38--AMPD1
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[197000] -fusion SPANNING read extraction for scaff: LRP1B--AC078882.1
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[67000] -fusion SPANNING read extraction for scaff: MB21D2--FGF12
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[30000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA8
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA10
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[19000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB6
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC5
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[20000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA11
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC4
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[14000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGB7
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[18000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA12
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[71000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGA9
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[218000] -fusion SPANNING read extraction for scaff: PCDHGB2--PCDHGC3
[1000]
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[39000] -fusion SPANNING read extraction for scaff: RNA5SP281--ACO1
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[43000] -fusion SPANNING read extraction for scaff: RNA5SP56--SPAG17
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[36000] -fusion SPANNING read extraction for scaff: TLK2--AC240565.1
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[7000] -fusion SPANNING read extraction for scaff: TLK2P1--AC110079.1
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[39000] -fusion SPANNING read extraction for scaff: TMED7--TICAM2
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[21000] -fusion SPANNING read extraction for scaff: TVP23C--CDRT4
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[23000] -fusion SPANNING read extraction for scaff: ZKSCAN7--KIF15
-filtered reads reasons: $VAR1 = {
'seq similar region alignment' => 32589,
'lacks exon overlap' => 32167
};
Execution Time = 3.83 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_fusion_SPANNING_reads_from_bam.from_chim_summary.pl --gtf_file /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --MIN_ALIGN_PER_ID 96 --bam /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam --junction_info /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/get_fusion_SPANNING_reads_from_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/coalesce_junction_and_spanning_info.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junction_info /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_spanning_info 1 > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/coalesce_junc_n_span.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
EM: Starting log likelihood: -8636.895261
EM: Round [1] log likelihood: -8629.873389
EM: Round [2] log likelihood: -8629.865698
EM: Round [3] log likelihood: -8629.861749
EM: Round [4] log likelihood: -8629.857826
EM: Round [5] log likelihood: -8629.853921
EM: Round [6] log likelihood: -8629.850032
EM: Round [7] log likelihood: -8629.846161
EM: Round [8] log likelihood: -8629.842306
EM: Round [9] log likelihood: -8629.838467
EM: Round [10] log likelihood: -8629.834645
EM: Round [11] log likelihood: -8629.830839
EM: Round [12] log likelihood: -8629.827049
EM: Round [13] log likelihood: -8629.823275
EM: Round [14] log likelihood: -8629.819517
EM: Round [15] log likelihood: -8629.815775
EM: Round [16] log likelihood: -8629.812049
EM: Round [17] log likelihood: -8629.808337
EM: Round [18] log likelihood: -8629.804642
EM: Round [19] log likelihood: -8629.800961
EM: Round [20] log likelihood: -8629.797296
EM: Round [21] log likelihood: -8629.793645
EM: Round [22] log likelihood: -8629.790010
EM: Round [23] log likelihood: -8629.786389
EM: Round [24] log likelihood: -8629.782783
EM: Round [25] log likelihood: -8629.779191
EM: Round [26] log likelihood: -8629.775614
EM: Round [27] log likelihood: -8629.772051
EM: Round [28] log likelihood: -8629.768503
EM: Round [29] log likelihood: -8629.764968
EM: Round [30] log likelihood: -8629.761448
EM: Round [31] log likelihood: -8629.757941
EM: Round [32] log likelihood: -8629.754449
EM: Round [33] log likelihood: -8629.750970
EM: Round [34] log likelihood: -8629.747504
EM: Round [35] log likelihood: -8629.744052
EM: Round [36] log likelihood: -8629.740614
EM: Round [37] log likelihood: -8629.737189
EM: Round [38] log likelihood: -8629.733777
EM: Round [39] log likelihood: -8629.730378
EM: Round [40] log likelihood: -8629.726992
EM: Round [41] log likelihood: -8629.723619
EM: Round [42] log likelihood: -8629.720259
EM: Round [43] log likelihood: -8629.716911
EM: Round [44] log likelihood: -8629.713577
EM: Round [45] log likelihood: -8629.710255
EM: Round [46] log likelihood: -8629.706945
EM: Round [47] log likelihood: -8629.703648
EM: Round [48] log likelihood: -8629.700363
EM: Round [49] log likelihood: -8629.697090
EM: Round [50] log likelihood: -8629.693829
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EM: Round [968] log likelihood: -8628.454519
EM: Round [969] log likelihood: -8628.453893
EM: Round [970] log likelihood: -8628.453267
EM: Round [971] log likelihood: -8628.452642
EM: Round [972] log likelihood: -8628.452018
EM: Round [973] log likelihood: -8628.451394
EM: Round [974] log likelihood: -8628.450771
EM: Round [975] log likelihood: -8628.450149
EM: Round [976] log likelihood: -8628.449527
EM: Round [977] log likelihood: -8628.448906
EM: Round [978] log likelihood: -8628.448286
EM: Round [979] log likelihood: -8628.447666
EM: Round [980] log likelihood: -8628.447047
EM: Round [981] log likelihood: -8628.446429
EM: Round [982] log likelihood: -8628.445811
EM: Round [983] log likelihood: -8628.445194
EM: Round [984] log likelihood: -8628.444578
EM: Round [985] log likelihood: -8628.443962
EM: Round [986] log likelihood: -8628.443347
EM: Round [987] log likelihood: -8628.442732
EM: Round [988] log likelihood: -8628.442119
EM: Round [989] log likelihood: -8628.441505
EM: Round [990] log likelihood: -8628.440893
EM: Round [991] log likelihood: -8628.440281
EM: Round [992] log likelihood: -8628.439670
EM: Round [993] log likelihood: -8628.439059
EM: Round [994] log likelihood: -8628.438449
EM: Round [995] log likelihood: -8628.437840
EM: Round [996] log likelihood: -8628.437231
EM: Round [997] log likelihood: -8628.436623
EM: Round [998] log likelihood: -8628.436016
EM: Round [999] log likelihood: -8628.435409
EM: Round [1000] log likelihood: -8628.434803
EM: Round [1001] log likelihood: -8628.434198
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/init_EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/filter_fusions_by_frag_thresholds.pl --min_junction_reads 0 --min_sum_frags 1 --min_novel_junction_support 3 --min_spanning_frags_only 5 --fusion_preds /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj --require_LDAS 1 > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/filter_by_frag_threshs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,JunctionReads > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_extract_junc_reads.ok
Running: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam"
[bam_sort_core] merging from 0 files and 8 in-memory blocks...
Execution Time = 0.01 minutes. CMD: bash -c "set -eof pipefail; /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_junction_reads_by_accession.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_junction_read_accs /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_junc_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam"
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_junc_reads_bam.ok
Running: samtools index /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/samtools_idx_junc_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.junction_reads.bam.tabix.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_extractions.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary LeftGene,RightGene,SpanningFrags > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/span_reads_acc.ok
Running: samtools view -H /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools view -H /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam -b -o /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/init_spanning_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam || :
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/retrieve_fusion_spanning_reads_by_accession.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.fusion_spanning_read_accs /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam.fusion_span_reads.sam | samtools view -@ 8 -bT /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa - | samtools sort -@ 8 - -o /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam || :
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_spanning_reads.ok
Running: samtools index /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Execution Time = 0.00 minutes. CMD: samtools index /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/samtools_index_span_reads_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_pair_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bam_to_bed.ok
Running: sort -k1,1 -k2,2n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: sort -k1,1 -k2,2n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bedsort.ok
Running: bgzip -f /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Execution Time = 0.00 minutes. CMD: bgzip -f /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bgzip.ok
Running: tabix -p bed /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Execution Time = 0.00 minutes. CMD: tabix -p bed /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.bed.sorted.bed.gz
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.spanning_reads.bam.tabix.ok
Running: cp /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.star.cSorted.dupsMarked.bam /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/cp_consol_bam.ok
Running: samtools index /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Execution Time = 0.03 minutes. CMD: samtools index /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/index_consol_bam.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000
-extracting read coordinates from /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam into /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords
CMD: touch /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.ok
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k2,2 -k4,4n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.read_coords.sort_by_readname
CMD: /usr/bin/sort --parallel=1 -S10G -T . -k1,1 -k3,3n /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords.coord_sorted
Execution Time = 0.65 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/SAM_to_frag_coords.pl --sam /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam --max_insert_size 10000000
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_sam_frag_coordss.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan
Execution Time = 0.01 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_summary_to_igv_JuncSpan_fmt.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.consolidated.bam.frag_coords > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.FusionJuncSpan
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_juncspan_fmt.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_pfam_domain_info.pl --finspector_gtf /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_pfam_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.gff3 > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.Pfam.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_pfam_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/get_seq_similar_region_FI_coordinates.pl --finspector_gtf /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf --genome_lib_dir ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_seqsim_gff3.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/transcript_gff3_to_bed.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.gff3 > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.igv.seqsimilar.bed
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/prep_igv_seqsim_bed.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/append_breakpoint_junction_info_via_FI_contigs.pl /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa > /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/add_splice_info.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/blast_filter.pl --fusion_preds /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --genome_lib_dir ctat_genome_lib_build_dir
CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionFilter/util/promiscuity_filter.pl --fusion_preds /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
CMD: cp /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo.post_blast_filter.post_promisc_filter /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/blast_and_promiscuity_filter.pl --fusion_preds /tmp/nxf.bIDYTem8xp/fi_workdir/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_preds.coalesced.summary.EMadj.min_frag_thresh.wSpliceInfo --out_prefix /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1 --genome_lib_dir ctat_genome_lib_build_dir --max_promiscuity 10 --min_pct_dom_promiscuity 50
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/blast_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir
-done, see /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/../FusionFilter/util/filter_by_annotation_rules.pl --fusions /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter --genome_lib_dir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/annot_filter.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
EM: Starting log likelihood: -8170.064007
EM: Round [1] log likelihood: -8169.422296
EM: Round [2] log likelihood: -8169.417938
EM: Round [3] log likelihood: -8169.414856
EM: Round [4] log likelihood: -8169.411793
EM: Round [5] log likelihood: -8169.408741
EM: Round [6] log likelihood: -8169.405700
EM: Round [7] log likelihood: -8169.402669
EM: Round [8] log likelihood: -8169.399649
EM: Round [9] log likelihood: -8169.396639
EM: Round [10] log likelihood: -8169.393639
EM: Round [11] log likelihood: -8169.390650
EM: Round [12] log likelihood: -8169.387671
EM: Round [13] log likelihood: -8169.384702
EM: Round [14] log likelihood: -8169.381743
EM: Round [15] log likelihood: -8169.378795
EM: Round [16] log likelihood: -8169.375856
EM: Round [17] log likelihood: -8169.372927
EM: Round [18] log likelihood: -8169.370008
EM: Round [19] log likelihood: -8169.367099
EM: Round [20] log likelihood: -8169.364199
EM: Round [21] log likelihood: -8169.361310
EM: Round [22] log likelihood: -8169.358429
EM: Round [23] log likelihood: -8169.355559
EM: Round [24] log likelihood: -8169.352698
EM: Round [25] log likelihood: -8169.349846
EM: Round [26] log likelihood: -8169.347004
EM: Round [27] log likelihood: -8169.344170
EM: Round [28] log likelihood: -8169.341347
EM: Round [29] log likelihood: -8169.338532
EM: Round [30] log likelihood: -8169.335727
EM: Round [31] log likelihood: -8169.332930
EM: Round [32] log likelihood: -8169.330143
EM: Round [33] log likelihood: -8169.327365
EM: Round [34] log likelihood: -8169.324595
EM: Round [35] log likelihood: -8169.321835
EM: Round [36] log likelihood: -8169.319083
EM: Round [37] log likelihood: -8169.316340
EM: Round [38] log likelihood: -8169.313606
EM: Round [39] log likelihood: -8169.310880
EM: Round [40] log likelihood: -8169.308163
EM: Round [41] log likelihood: -8169.305455
EM: Round [42] log likelihood: -8169.302755
EM: Round [43] log likelihood: -8169.300064
EM: Round [44] log likelihood: -8169.297381
EM: Round [45] log likelihood: -8169.294706
EM: Round [46] log likelihood: -8169.292040
EM: Round [47] log likelihood: -8169.289382
EM: Round [48] log likelihood: -8169.286732
EM: Round [49] log likelihood: -8169.284090
EM: Round [50] log likelihood: -8169.281457
EM: Round [51] log likelihood: -8169.278831
EM: Round [52] log likelihood: -8169.276214
EM: Round [53] log likelihood: -8169.273604
EM: Round [54] log likelihood: -8169.271003
EM: Round [55] log likelihood: -8169.268409
EM: Round [56] log likelihood: -8169.265824
EM: Round [57] log likelihood: -8169.263246
EM: Round [58] log likelihood: -8169.260676
EM: Round [59] log likelihood: -8169.258113
EM: Round [60] log likelihood: -8169.255559
EM: Round [61] log likelihood: -8169.253012
EM: Round [62] log likelihood: -8169.250472
EM: Round [63] log likelihood: -8169.247940
EM: Round [64] log likelihood: -8169.245416
EM: Round [65] log likelihood: -8169.242899
EM: Round [66] log likelihood: -8169.240390
EM: Round [67] log likelihood: -8169.237887
EM: Round [68] log likelihood: -8169.235393
EM: Round [69] log likelihood: -8169.232905
EM: Round [70] log likelihood: -8169.230425
EM: Round [71] log likelihood: -8169.227952
EM: Round [72] log likelihood: -8169.225487
EM: Round [73] log likelihood: -8169.223028
EM: Round [74] log likelihood: -8169.220577
EM: Round [75] log likelihood: -8169.218132
EM: Round [76] log likelihood: -8169.215695
EM: Round [77] log likelihood: -8169.213265
EM: Round [78] log likelihood: -8169.210841
EM: Round [79] log likelihood: -8169.208425
EM: Round [80] log likelihood: -8169.206015
EM: Round [81] log likelihood: -8169.203613
EM: Round [82] log likelihood: -8169.201217
EM: Round [83] log likelihood: -8169.198828
EM: Round [84] log likelihood: -8169.196445
EM: Round [85] log likelihood: -8169.194070
EM: Round [86] log likelihood: -8169.191701
EM: Round [87] log likelihood: -8169.189339
EM: Round [88] log likelihood: -8169.186983
EM: Round [89] log likelihood: -8169.184634
EM: Round [90] log likelihood: -8169.182292
EM: Round [91] log likelihood: -8169.179956
EM: Round [92] log likelihood: -8169.177626
EM: Round [93] log likelihood: -8169.175303
EM: Round [94] log likelihood: -8169.172986
EM: Round [95] log likelihood: -8169.170676
EM: Round [96] log likelihood: -8169.168372
EM: Round [97] log likelihood: -8169.166074
EM: Round [98] log likelihood: -8169.163783
EM: Round [99] log likelihood: -8169.161498
EM: Round [100] log likelihood: -8169.159219
EM: Round [101] log likelihood: -8169.156946
EM: Round [102] log likelihood: -8169.154680
EM: Round [103] log likelihood: -8169.152420
EM: Round [104] log likelihood: -8169.150165
EM: Round [105] log likelihood: -8169.147917
EM: Round [106] log likelihood: -8169.145675
EM: Round [107] log likelihood: -8169.143439
EM: Round [108] log likelihood: -8169.141209
EM: Round [109] log likelihood: -8169.138984
EM: Round [110] log likelihood: -8169.136766
EM: Round [111] log likelihood: -8169.134554
EM: Round [112] log likelihood: -8169.132347
EM: Round [113] log likelihood: -8169.130146
EM: Round [114] log likelihood: -8169.127951
EM: Round [115] log likelihood: -8169.125762
EM: Round [116] log likelihood: -8169.123579
EM: Round [117] log likelihood: -8169.121401
EM: Round [118] log likelihood: -8169.119229
EM: Round [119] log likelihood: -8169.117063
EM: Round [120] log likelihood: -8169.114902
EM: Round [121] log likelihood: -8169.112747
EM: Round [122] log likelihood: -8169.110598
EM: Round [123] log likelihood: -8169.108454
EM: Round [124] log likelihood: -8169.106316
EM: Round [125] log likelihood: -8169.104183
EM: Round [126] log likelihood: -8169.102056
EM: Round [127] log likelihood: -8169.099934
EM: Round [128] log likelihood: -8169.097817
EM: Round [129] log likelihood: -8169.095706
EM: Round [130] log likelihood: -8169.093600
EM: Round [131] log likelihood: -8169.091500
EM: Round [132] log likelihood: -8169.089405
EM: Round [133] log likelihood: -8169.087316
EM: Round [134] log likelihood: -8169.085231
EM: Round [135] log likelihood: -8169.083152
EM: Round [136] log likelihood: -8169.081078
EM: Round [137] log likelihood: -8169.079009
EM: Round [138] log likelihood: -8169.076946
EM: Round [139] log likelihood: -8169.074888
EM: Round [140] log likelihood: -8169.072834
EM: Round [141] log likelihood: -8169.070786
EM: Round [142] log likelihood: -8169.068743
EM: Round [143] log likelihood: -8169.066705
EM: Round [144] log likelihood: -8169.064673
EM: Round [145] log likelihood: -8169.062645
EM: Round [146] log likelihood: -8169.060622
EM: Round [147] log likelihood: -8169.058604
EM: Round [148] log likelihood: -8169.056591
EM: Round [149] log likelihood: -8169.054583
EM: Round [150] log likelihood: -8169.052580
EM: Round [151] log likelihood: -8169.050582
EM: Round [152] log likelihood: -8169.048589
EM: Round [153] log likelihood: -8169.046600
EM: Round [154] log likelihood: -8169.044617
EM: Round [155] log likelihood: -8169.042638
EM: Round [156] log likelihood: -8169.040664
EM: Round [157] log likelihood: -8169.038695
EM: Round [158] log likelihood: -8169.036730
EM: Round [159] log likelihood: -8169.034770
EM: Round [160] log likelihood: -8169.032815
EM: Round [161] log likelihood: -8169.030865
EM: Round [162] log likelihood: -8169.028919
EM: Round [163] log likelihood: -8169.026978
EM: Round [164] log likelihood: -8169.025041
EM: Round [165] log likelihood: -8169.023110
EM: Round [166] log likelihood: -8169.021182
EM: Round [167] log likelihood: -8169.019260
EM: Round [168] log likelihood: -8169.017341
EM: Round [169] log likelihood: -8169.015428
EM: Round [170] log likelihood: -8169.013518
EM: Round [171] log likelihood: -8169.011614
EM: Round [172] log likelihood: -8169.009714
EM: Round [173] log likelihood: -8169.007818
EM: Round [174] log likelihood: -8169.005926
EM: Round [175] log likelihood: -8169.004039
EM: Round [176] log likelihood: -8169.002157
EM: Round [177] log likelihood: -8169.000279
EM: Round [178] log likelihood: -8168.998405
EM: Round [179] log likelihood: -8168.996535
EM: Round [180] log likelihood: -8168.994670
EM: Round [181] log likelihood: -8168.992809
EM: Round [182] log likelihood: -8168.990953
EM: Round [183] log likelihood: -8168.989100
EM: Round [184] log likelihood: -8168.987252
EM: Round [185] log likelihood: -8168.985409
EM: Round [186] log likelihood: -8168.983569
EM: Round [187] log likelihood: -8168.981733
EM: Round [188] log likelihood: -8168.979902
EM: Round [189] log likelihood: -8168.978075
EM: Round [190] log likelihood: -8168.976252
EM: Round [191] log likelihood: -8168.974433
EM: Round [192] log likelihood: -8168.972618
EM: Round [193] log likelihood: -8168.970808
EM: Round [194] log likelihood: -8168.969001
EM: Round [195] log likelihood: -8168.967199
EM: Round [196] log likelihood: -8168.965400
EM: Round [197] log likelihood: -8168.963606
EM: Round [198] log likelihood: -8168.961815
EM: Round [199] log likelihood: -8168.960029
EM: Round [200] log likelihood: -8168.958246
EM: Round [201] log likelihood: -8168.956468
EM: Round [202] log likelihood: -8168.954693
EM: Round [203] log likelihood: -8168.952923
EM: Round [204] log likelihood: -8168.951156
EM: Round [205] log likelihood: -8168.949393
EM: Round [206] log likelihood: -8168.947634
EM: Round [207] log likelihood: -8168.945879
EM: Round [208] log likelihood: -8168.944128
EM: Round [209] log likelihood: -8168.942381
EM: Round [210] log likelihood: -8168.940637
EM: Round [211] log likelihood: -8168.938897
EM: Round [212] log likelihood: -8168.937161
EM: Round [213] log likelihood: -8168.935429
EM: Round [214] log likelihood: -8168.933701
EM: Round [215] log likelihood: -8168.931976
EM: Round [216] log likelihood: -8168.930255
EM: Round [217] log likelihood: -8168.928538
EM: Round [218] log likelihood: -8168.926825
EM: Round [219] log likelihood: -8168.925115
EM: Round [220] log likelihood: -8168.923409
EM: Round [221] log likelihood: -8168.921706
EM: Round [222] log likelihood: -8168.920007
EM: Round [223] log likelihood: -8168.918312
EM: Round [224] log likelihood: -8168.916620
EM: Round [225] log likelihood: -8168.914933
EM: Round [226] log likelihood: -8168.913248
EM: Round [227] log likelihood: -8168.911567
EM: Round [228] log likelihood: -8168.909890
EM: Round [229] log likelihood: -8168.908216
EM: Round [230] log likelihood: -8168.906546
EM: Round [231] log likelihood: -8168.904880
EM: Round [232] log likelihood: -8168.903217
EM: Round [233] log likelihood: -8168.901557
EM: Round [234] log likelihood: -8168.899901
EM: Round [235] log likelihood: -8168.898248
EM: Round [236] log likelihood: -8168.896599
EM: Round [237] log likelihood: -8168.894953
EM: Round [238] log likelihood: -8168.893311
EM: Round [239] log likelihood: -8168.891672
EM: Round [240] log likelihood: -8168.890037
EM: Round [241] log likelihood: -8168.888405
EM: Round [242] log likelihood: -8168.886776
EM: Round [243] log likelihood: -8168.885151
EM: Round [244] log likelihood: -8168.883529
EM: Round [245] log likelihood: -8168.881910
EM: Round [246] log likelihood: -8168.880295
EM: Round [247] log likelihood: -8168.878683
EM: Round [248] log likelihood: -8168.877074
EM: Round [249] log likelihood: -8168.875469
EM: Round [250] log likelihood: -8168.873867
EM: Round [251] log likelihood: -8168.872268
EM: Round [252] log likelihood: -8168.870672
EM: Round [253] log likelihood: -8168.869080
EM: Round [254] log likelihood: -8168.867491
EM: Round [255] log likelihood: -8168.865905
EM: Round [256] log likelihood: -8168.864322
EM: Round [257] log likelihood: -8168.862743
EM: Round [258] log likelihood: -8168.861167
EM: Round [259] log likelihood: -8168.859594
EM: Round [260] log likelihood: -8168.858024
EM: Round [261] log likelihood: -8168.856457
EM: Round [262] log likelihood: -8168.854894
EM: Round [263] log likelihood: -8168.853333
EM: Round [264] log likelihood: -8168.851776
EM: Round [265] log likelihood: -8168.850222
EM: Round [266] log likelihood: -8168.848671
EM: Round [267] log likelihood: -8168.847123
EM: Round [268] log likelihood: -8168.845578
EM: Round [269] log likelihood: -8168.844036
EM: Round [270] log likelihood: -8168.842497
EM: Round [271] log likelihood: -8168.840961
EM: Round [272] log likelihood: -8168.839428
EM: Round [273] log likelihood: -8168.837899
EM: Round [274] log likelihood: -8168.836372
EM: Round [275] log likelihood: -8168.834848
EM: Round [276] log likelihood: -8168.833328
EM: Round [277] log likelihood: -8168.831810
EM: Round [278] log likelihood: -8168.830295
EM: Round [279] log likelihood: -8168.828783
EM: Round [280] log likelihood: -8168.827275
EM: Round [281] log likelihood: -8168.825769
EM: Round [282] log likelihood: -8168.824266
EM: Round [283] log likelihood: -8168.822766
EM: Round [284] log likelihood: -8168.821269
EM: Round [285] log likelihood: -8168.819774
EM: Round [286] log likelihood: -8168.818283
EM: Round [287] log likelihood: -8168.816795
EM: Round [288] log likelihood: -8168.815309
EM: Round [289] log likelihood: -8168.813826
EM: Round [290] log likelihood: -8168.812347
EM: Round [291] log likelihood: -8168.810870
EM: Round [292] log likelihood: -8168.809395
EM: Round [293] log likelihood: -8168.807924
EM: Round [294] log likelihood: -8168.806456
EM: Round [295] log likelihood: -8168.804990
EM: Round [296] log likelihood: -8168.803527
EM: Round [297] log likelihood: -8168.802067
EM: Round [298] log likelihood: -8168.800609
EM: Round [299] log likelihood: -8168.799155
EM: Round [300] log likelihood: -8168.797703
EM: Round [301] log likelihood: -8168.796254
EM: Round [302] log likelihood: -8168.794807
EM: Round [303] log likelihood: -8168.793364
EM: Round [304] log likelihood: -8168.791923
EM: Round [305] log likelihood: -8168.790485
EM: Round [306] log likelihood: -8168.789049
EM: Round [307] log likelihood: -8168.787616
EM: Round [308] log likelihood: -8168.786186
EM: Round [309] log likelihood: -8168.784759
EM: Round [310] log likelihood: -8168.783334
EM: Round [311] log likelihood: -8168.781912
EM: Round [312] log likelihood: -8168.780493
EM: Round [313] log likelihood: -8168.779076
EM: Round [314] log likelihood: -8168.777662
EM: Round [315] log likelihood: -8168.776250
EM: Round [316] log likelihood: -8168.774841
EM: Round [317] log likelihood: -8168.773435
EM: Round [318] log likelihood: -8168.772031
EM: Round [319] log likelihood: -8168.770630
EM: Round [320] log likelihood: -8168.769231
EM: Round [321] log likelihood: -8168.767835
EM: Round [322] log likelihood: -8168.766442
EM: Round [323] log likelihood: -8168.765051
EM: Round [324] log likelihood: -8168.763663
EM: Round [325] log likelihood: -8168.762277
EM: Round [326] log likelihood: -8168.760894
EM: Round [327] log likelihood: -8168.759513
EM: Round [328] log likelihood: -8168.758135
EM: Round [329] log likelihood: -8168.756759
EM: Round [330] log likelihood: -8168.755386
EM: Round [331] log likelihood: -8168.754015
EM: Round [332] log likelihood: -8168.752647
EM: Round [333] log likelihood: -8168.751281
EM: Round [334] log likelihood: -8168.749918
EM: Round [335] log likelihood: -8168.748557
EM: Round [336] log likelihood: -8168.747199
EM: Round [337] log likelihood: -8168.745843
EM: Round [338] log likelihood: -8168.744489
EM: Round [339] log likelihood: -8168.743138
EM: Round [340] log likelihood: -8168.741790
EM: Round [341] log likelihood: -8168.740443
EM: Round [342] log likelihood: -8168.739100
EM: Round [343] log likelihood: -8168.737758
EM: Round [344] log likelihood: -8168.736419
EM: Round [345] log likelihood: -8168.735083
EM: Round [346] log likelihood: -8168.733748
EM: Round [347] log likelihood: -8168.732416
EM: Round [348] log likelihood: -8168.731087
EM: Round [349] log likelihood: -8168.729760
EM: Round [350] log likelihood: -8168.728435
EM: Round [351] log likelihood: -8168.727112
EM: Round [352] log likelihood: -8168.725792
EM: Round [353] log likelihood: -8168.724475
EM: Round [354] log likelihood: -8168.723159
EM: Round [355] log likelihood: -8168.721846
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EM: Round [815] log likelihood: -8168.286287
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EM: Round [817] log likelihood: -8168.284905
EM: Round [818] log likelihood: -8168.284215
EM: Round [819] log likelihood: -8168.283526
EM: Round [820] log likelihood: -8168.282838
EM: Round [821] log likelihood: -8168.282150
EM: Round [822] log likelihood: -8168.281463
EM: Round [823] log likelihood: -8168.280777
EM: Round [824] log likelihood: -8168.280092
EM: Round [825] log likelihood: -8168.279408
EM: Round [826] log likelihood: -8168.278724
EM: Round [827] log likelihood: -8168.278041
EM: Round [828] log likelihood: -8168.277359
EM: Round [829] log likelihood: -8168.276678
EM: Round [830] log likelihood: -8168.275998
EM: Round [831] log likelihood: -8168.275318
EM: Round [832] log likelihood: -8168.274639
EM: Round [833] log likelihood: -8168.273960
EM: Round [834] log likelihood: -8168.273283
EM: Round [835] log likelihood: -8168.272606
EM: Round [836] log likelihood: -8168.271930
EM: Round [837] log likelihood: -8168.271255
EM: Round [838] log likelihood: -8168.270581
EM: Round [839] log likelihood: -8168.269907
EM: Round [840] log likelihood: -8168.269234
EM: Round [841] log likelihood: -8168.268562
EM: Round [842] log likelihood: -8168.267890
EM: Round [843] log likelihood: -8168.267220
EM: Round [844] log likelihood: -8168.266550
EM: Round [845] log likelihood: -8168.265880
EM: Round [846] log likelihood: -8168.265212
EM: Round [847] log likelihood: -8168.264544
EM: Round [848] log likelihood: -8168.263877
EM: Round [849] log likelihood: -8168.263211
EM: Round [850] log likelihood: -8168.262546
EM: Round [851] log likelihood: -8168.261881
EM: Round [852] log likelihood: -8168.261217
EM: Round [853] log likelihood: -8168.260553
EM: Round [854] log likelihood: -8168.259891
EM: Round [855] log likelihood: -8168.259229
EM: Round [856] log likelihood: -8168.258568
EM: Round [857] log likelihood: -8168.257908
EM: Round [858] log likelihood: -8168.257248
EM: Round [859] log likelihood: -8168.256589
EM: Round [860] log likelihood: -8168.255931
EM: Round [861] log likelihood: -8168.255273
EM: Round [862] log likelihood: -8168.254617
EM: Round [863] log likelihood: -8168.253961
EM: Round [864] log likelihood: -8168.253305
EM: Round [865] log likelihood: -8168.252651
EM: Round [866] log likelihood: -8168.251997
EM: Round [867] log likelihood: -8168.251344
EM: Round [868] log likelihood: -8168.250691
EM: Round [869] log likelihood: -8168.250040
EM: Round [870] log likelihood: -8168.249389
EM: Round [871] log likelihood: -8168.248739
EM: Round [872] log likelihood: -8168.248089
EM: Round [873] log likelihood: -8168.247440
EM: Round [874] log likelihood: -8168.246792
EM: Round [875] log likelihood: -8168.246145
EM: Round [876] log likelihood: -8168.245498
EM: Round [877] log likelihood: -8168.244852
EM: Round [878] log likelihood: -8168.244206
EM: Round [879] log likelihood: -8168.243562
EM: Round [880] log likelihood: -8168.242918
EM: Round [881] log likelihood: -8168.242275
EM: Round [882] log likelihood: -8168.241632
EM: Round [883] log likelihood: -8168.240990
EM: Round [884] log likelihood: -8168.240349
EM: Round [885] log likelihood: -8168.239709
EM: Round [886] log likelihood: -8168.239069
EM: Round [887] log likelihood: -8168.238430
EM: Round [888] log likelihood: -8168.237792
EM: Round [889] log likelihood: -8168.237154
EM: Round [890] log likelihood: -8168.236517
EM: Round [891] log likelihood: -8168.235881
EM: Round [892] log likelihood: -8168.235245
EM: Round [893] log likelihood: -8168.234610
EM: Round [894] log likelihood: -8168.233976
EM: Round [895] log likelihood: -8168.233343
EM: Round [896] log likelihood: -8168.232710
EM: Round [897] log likelihood: -8168.232078
EM: Round [898] log likelihood: -8168.231446
EM: Round [899] log likelihood: -8168.230815
EM: Round [900] log likelihood: -8168.230185
EM: Round [901] log likelihood: -8168.229556
EM: Round [902] log likelihood: -8168.228927
EM: Round [903] log likelihood: -8168.228299
EM: Round [904] log likelihood: -8168.227671
EM: Round [905] log likelihood: -8168.227045
EM: Round [906] log likelihood: -8168.226418
EM: Round [907] log likelihood: -8168.225793
EM: Round [908] log likelihood: -8168.225168
EM: Round [909] log likelihood: -8168.224544
EM: Round [910] log likelihood: -8168.223921
EM: Round [911] log likelihood: -8168.223298
EM: Round [912] log likelihood: -8168.222676
EM: Round [913] log likelihood: -8168.222055
EM: Round [914] log likelihood: -8168.221434
EM: Round [915] log likelihood: -8168.220814
EM: Round [916] log likelihood: -8168.220194
EM: Round [917] log likelihood: -8168.219575
EM: Round [918] log likelihood: -8168.218957
EM: Round [919] log likelihood: -8168.218340
EM: Round [920] log likelihood: -8168.217723
EM: Round [921] log likelihood: -8168.217107
EM: Round [922] log likelihood: -8168.216491
EM: Round [923] log likelihood: -8168.215876
EM: Round [924] log likelihood: -8168.215262
EM: Round [925] log likelihood: -8168.214649
EM: Round [926] log likelihood: -8168.214036
EM: Round [927] log likelihood: -8168.213424
EM: Round [928] log likelihood: -8168.212812
EM: Round [929] log likelihood: -8168.212201
EM: Round [930] log likelihood: -8168.211591
EM: Round [931] log likelihood: -8168.210981
EM: Round [932] log likelihood: -8168.210372
EM: Round [933] log likelihood: -8168.209764
EM: Round [934] log likelihood: -8168.209156
EM: Round [935] log likelihood: -8168.208549
EM: Round [936] log likelihood: -8168.207942
EM: Round [937] log likelihood: -8168.207336
EM: Round [938] log likelihood: -8168.206731
EM: Round [939] log likelihood: -8168.206127
EM: Round [940] log likelihood: -8168.205523
EM: Round [941] log likelihood: -8168.204919
EM: Round [942] log likelihood: -8168.204317
EM: Round [943] log likelihood: -8168.203715
EM: Round [944] log likelihood: -8168.203113
EM: Round [945] log likelihood: -8168.202512
EM: Round [946] log likelihood: -8168.201912
EM: Round [947] log likelihood: -8168.201313
EM: Round [948] log likelihood: -8168.200714
EM: Round [949] log likelihood: -8168.200115
EM: Round [950] log likelihood: -8168.199518
EM: Round [951] log likelihood: -8168.198921
EM: Round [952] log likelihood: -8168.198324
EM: Round [953] log likelihood: -8168.197729
EM: Round [954] log likelihood: -8168.197133
EM: Round [955] log likelihood: -8168.196539
EM: Round [956] log likelihood: -8168.195945
EM: Round [957] log likelihood: -8168.195352
EM: Round [958] log likelihood: -8168.194759
EM: Round [959] log likelihood: -8168.194167
EM: Round [960] log likelihood: -8168.193575
EM: Round [961] log likelihood: -8168.192984
EM: Round [962] log likelihood: -8168.192394
EM: Round [963] log likelihood: -8168.191804
EM: Round [964] log likelihood: -8168.191215
EM: Round [965] log likelihood: -8168.190627
EM: Round [966] log likelihood: -8168.190039
EM: Round [967] log likelihood: -8168.189452
EM: Round [968] log likelihood: -8168.188865
EM: Round [969] log likelihood: -8168.188279
EM: Round [970] log likelihood: -8168.187694
EM: Round [971] log likelihood: -8168.187109
EM: Round [972] log likelihood: -8168.186525
EM: Round [973] log likelihood: -8168.185941
EM: Round [974] log likelihood: -8168.185358
EM: Round [975] log likelihood: -8168.184776
EM: Round [976] log likelihood: -8168.184194
EM: Round [977] log likelihood: -8168.183613
EM: Round [978] log likelihood: -8168.183032
EM: Round [979] log likelihood: -8168.182452
EM: Round [980] log likelihood: -8168.181873
EM: Round [981] log likelihood: -8168.181294
EM: Round [982] log likelihood: -8168.180716
EM: Round [983] log likelihood: -8168.180138
EM: Round [984] log likelihood: -8168.179561
EM: Round [985] log likelihood: -8168.178985
EM: Round [986] log likelihood: -8168.178409
EM: Round [987] log likelihood: -8168.177833
EM: Round [988] log likelihood: -8168.177259
EM: Round [989] log likelihood: -8168.176685
EM: Round [990] log likelihood: -8168.176111
EM: Round [991] log likelihood: -8168.175538
EM: Round [992] log likelihood: -8168.174966
EM: Round [993] log likelihood: -8168.174394
EM: Round [994] log likelihood: -8168.173823
EM: Round [995] log likelihood: -8168.173252
EM: Round [996] log likelihood: -8168.172682
EM: Round [997] log likelihood: -8168.172113
EM: Round [998] log likelihood: -8168.171544
EM: Round [999] log likelihood: -8168.170975
EM: Round [1000] log likelihood: -8168.170408
EM: Round [1001] log likelihood: -8168.169841
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_EM_runner.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/EM_adj_counts.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
-total frags in /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz: 294468379
Execution Time = 5.97 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/incorporate_FFPM_into_final_report.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1_1.fastp.fastq.gz /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/add_FFPM.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.bIDYTem8xp/fi_workdir/microH.dat
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/find_microhomologies_by_kmer_matches.pl --fasta /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fa --gtf /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gtf > /tmp/nxf.bIDYTem8xp/fi_workdir/microH.dat
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/microH.dat.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.bIDYTem8xp/fi_workdir/microH.dat /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/misc/append_microH_distance.py /tmp/nxf.bIDYTem8xp/fi_workdir/microH.dat /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/append_microH_info.ok
Running: cp /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv
Execution Time = 0.00 minutes. CMD: cp /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.post_blast_and_promiscuity_filter.annot_filter.pass.EMadj.FFPM.wMicroH /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/cp_final.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/column_exclusions.pl /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.tsv JunctionReads,SpanningFrags,CounterFusionLeftReads,CounterFusionRightReads > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/final.abridged.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.bIDYTem8xp --json_outfile /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/util/create_fusion_inspector_igvjs.py --fusion_inspector_directory /tmp/nxf.bIDYTem8xp --json_outfile /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/create_fi_igvjs.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html
Warning - not locating file: /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.gmap_trinity_GG.fusions.gff3.bed
Execution Time = 0.02 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/fusion-reports/create_fusion_report.py --html_template /usr/local/src/STAR-Fusion/FusionInspector/util/fusion_report_html_template/igvjs_fusion.html --fusions_json /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.json --input_file_prefix 786-O_FFPE_RNA_0001_B23LG7FLT4_1 --html_output /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.fusion_inspector_web.html
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/fusion_reports_html.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/FusionAnnotator --annotate /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv --genome_lib_dir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/fusion_annotator.ok
Running: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
WARNING, no entry stored in dbm for [ENSG00000280136.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000285169.2]
WARNING, no entry stored in dbm for [ENSG00000226049.3]
WARNING, no entry stored in dbm for [ENSG00000260404.3]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
WARNING, no entry stored in dbm for [ENSG00000176593.8]
Execution Time = 0.00 minutes. CMD: /usr/local/src/STAR-Fusion/FusionInspector/FusionAnnotator/util/fusion_to_coding_region_effect.pl --fusions /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated --genome_lib_dir /tmp/nxf.bIDYTem8xp/ctat_genome_lib_build_dir > /tmp/nxf.bIDYTem8xp/786-O_FFPE_RNA_0001_B23LG7FLT4_1.FusionInspector.fusions.abridged.tsv.annotated.coding_effect
Running: touch /tmp/nxf.bIDYTem8xp/chckpts_dir/fusion_coding_region_effect.ok
ls: cannot access 'IGV_inputs': No such file or directory